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Attempt fixing segmentation fault on MacOS in GitHub Actions
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| Original file line number | Diff line number | Diff line change |
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@@ -6,111 +6,111 @@ on: | |
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| jobs: | ||
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| test_linux_x86: | ||
| name: Test (Linux) | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| OS: Linux | ||
| strategy: | ||
| matrix: | ||
| include: | ||
| - python-version: 3.7 | ||
| python-release: v3.7 | ||
| python-impl: CPython | ||
| - python-version: 3.8 | ||
| python-release: v3.8 | ||
| python-impl: CPython | ||
| - python-version: 3.9 | ||
| python-release: v3.9 | ||
| python-impl: CPython | ||
| - python-version: '3.10' | ||
| python-release: 'v3.10' | ||
| python-impl: CPython | ||
| - python-version: '3.11' | ||
| python-release: 'v3.11' | ||
| python-impl: CPython | ||
| - python-version: '3.12' | ||
| python-release: 'v3.12' | ||
| python-impl: CPython | ||
| - python-version: pypy-3.7 | ||
| python-release: v3.7 | ||
| python-impl: PyPy | ||
| - python-version: pypy-3.8 | ||
| python-release: v3.8 | ||
| python-impl: PyPy | ||
| - python-version: pypy-3.9 | ||
| python-release: v3.9 | ||
| python-impl: PyPy | ||
| steps: | ||
| - name: Checkout code | ||
| uses: actions/checkout@v2 | ||
| with: | ||
| submodules: true | ||
| - name: Cache Python requirements | ||
| uses: actions/cache@v2 | ||
| with: | ||
| path: ~/.cache/pip | ||
| key: ${{ runner.os }}-pip-${{ matrix.python-version }} | ||
| restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }} | ||
| - name: Setup Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Show Python build environment | ||
| run: python -m sysconfig | ||
| - name: Update pip | ||
| run: python -m pip install -U pip wheel setuptools | ||
| - name: Install Python requirements | ||
| run: python -m pip install -r .github/workflows/requirements.txt | ||
| - name: Build C extension | ||
| run: python setup.py build_ext --inplace --debug -j0 | ||
| - name: Install test requirements | ||
| run: python -m pip install -r pyhmmer/tests/requirements.txt | ||
| - name: Test with coverage | ||
| run: python -m coverage run -m unittest discover -vv | ||
| - name: Upload to Codecov | ||
| if: matrix.python-impl == 'CPython' | ||
| uses: codecov/codecov-action@v3 | ||
| with: | ||
| flags: ${{ matrix.python-release }} | ||
| env_vars: OS | ||
| name: test-python-${{ matrix.python-version }} | ||
| fail_ci_if_error: false | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| verbose: true | ||
|
|
||
| test_linux_arm64: | ||
| name: Test (Linux, arm64) | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-tag: | ||
| - cp310-manylinux_aarch64 | ||
| - cp311-manylinux_aarch64 | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| submodules: true | ||
| - name: Set up QEMU | ||
| id: qemu | ||
| uses: docker/setup-qemu-action@v2 | ||
| with: | ||
| platforms: all | ||
| - name: Build manylinux wheels | ||
| uses: pypa/[email protected] | ||
| env: | ||
| CIBW_ARCHS: aarch64 | ||
| CIBW_BUILD: ${{ matrix.python-tag }} | ||
| CIBW_BUILD_VERBOSITY: 2 | ||
| CIBW_BEFORE_BUILD: pip install cython | ||
| CIBW_TEST_COMMAND: python -m unittest pyhmmer.tests -vv | ||
| CIBW_TEST_REQUIRES: importlib-resources | ||
| with: | ||
| output-dir: dist | ||
| - uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: wheels | ||
| path: dist/* | ||
| # test_linux_x86: | ||
| # name: Test (Linux) | ||
| # runs-on: ubuntu-latest | ||
| # env: | ||
| # OS: Linux | ||
| # strategy: | ||
| # matrix: | ||
| # include: | ||
| # - python-version: 3.7 | ||
| # python-release: v3.7 | ||
| # python-impl: CPython | ||
| # - python-version: 3.8 | ||
| # python-release: v3.8 | ||
| # python-impl: CPython | ||
| # - python-version: 3.9 | ||
| # python-release: v3.9 | ||
| # python-impl: CPython | ||
| # - python-version: '3.10' | ||
| # python-release: 'v3.10' | ||
| # python-impl: CPython | ||
| # - python-version: '3.11' | ||
| # python-release: 'v3.11' | ||
| # python-impl: CPython | ||
| # - python-version: '3.12' | ||
| # python-release: 'v3.12' | ||
| # python-impl: CPython | ||
| # - python-version: pypy-3.7 | ||
| # python-release: v3.7 | ||
| # python-impl: PyPy | ||
| # - python-version: pypy-3.8 | ||
| # python-release: v3.8 | ||
| # python-impl: PyPy | ||
| # - python-version: pypy-3.9 | ||
| # python-release: v3.9 | ||
| # python-impl: PyPy | ||
| # steps: | ||
| # - name: Checkout code | ||
| # uses: actions/checkout@v2 | ||
| # with: | ||
| # submodules: true | ||
| # - name: Cache Python requirements | ||
| # uses: actions/cache@v2 | ||
| # with: | ||
| # path: ~/.cache/pip | ||
| # key: ${{ runner.os }}-pip-${{ matrix.python-version }} | ||
| # restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }} | ||
| # - name: Setup Python ${{ matrix.python-version }} | ||
| # uses: actions/setup-python@v2 | ||
| # with: | ||
| # python-version: ${{ matrix.python-version }} | ||
| # - name: Show Python build environment | ||
| # run: python -m sysconfig | ||
| # - name: Update pip | ||
| # run: python -m pip install -U pip wheel setuptools | ||
| # - name: Install Python requirements | ||
| # run: python -m pip install -r .github/workflows/requirements.txt | ||
| # - name: Build C extension | ||
| # run: python setup.py build_ext --inplace --debug -j0 | ||
| # - name: Install test requirements | ||
| # run: python -m pip install -r pyhmmer/tests/requirements.txt | ||
| # - name: Test with coverage | ||
| # run: python -m coverage run -m unittest discover -vv | ||
| # - name: Upload to Codecov | ||
| # if: matrix.python-impl == 'CPython' | ||
| # uses: codecov/codecov-action@v3 | ||
| # with: | ||
| # flags: ${{ matrix.python-release }} | ||
| # env_vars: OS | ||
| # name: test-python-${{ matrix.python-version }} | ||
| # fail_ci_if_error: false | ||
| # token: ${{ secrets.CODECOV_TOKEN }} | ||
| # verbose: true | ||
|
|
||
| # test_linux_arm64: | ||
| # name: Test (Linux, arm64) | ||
| # runs-on: ubuntu-latest | ||
| # strategy: | ||
| # matrix: | ||
| # python-tag: | ||
| # - cp310-manylinux_aarch64 | ||
| # - cp311-manylinux_aarch64 | ||
| # steps: | ||
| # - uses: actions/checkout@v3 | ||
| # with: | ||
| # submodules: true | ||
| # - name: Set up QEMU | ||
| # id: qemu | ||
| # uses: docker/setup-qemu-action@v2 | ||
| # with: | ||
| # platforms: all | ||
| # - name: Build manylinux wheels | ||
| # uses: pypa/[email protected] | ||
| # env: | ||
| # CIBW_ARCHS: aarch64 | ||
| # CIBW_BUILD: ${{ matrix.python-tag }} | ||
| # CIBW_BUILD_VERBOSITY: 2 | ||
| # CIBW_BEFORE_BUILD: pip install cython | ||
| # CIBW_TEST_COMMAND: python -m unittest pyhmmer.tests -vv | ||
| # CIBW_TEST_REQUIRES: importlib-resources | ||
| # with: | ||
| # output-dir: dist | ||
| # - uses: actions/upload-artifact@v3 | ||
| # with: | ||
| # name: wheels | ||
| # path: dist/* | ||
|
|
||
| test_osx_x86: | ||
| name: Test (OSX) | ||
|
|
@@ -121,33 +121,33 @@ jobs: | |
| strategy: | ||
| matrix: | ||
| include: | ||
| - python-version: 3.7 | ||
| python-release: v3.7 | ||
| python-impl: CPython | ||
| - python-version: 3.8 | ||
| python-release: v3.8 | ||
| python-impl: CPython | ||
| - python-version: 3.9 | ||
| python-release: v3.9 | ||
| python-impl: CPython | ||
| - python-version: '3.10' | ||
| python-release: 'v3.10' | ||
| python-impl: CPython | ||
| - python-version: '3.11' | ||
| python-release: 'v3.11' | ||
| python-impl: CPython | ||
| # - python-version: 3.7 | ||
| # python-release: v3.7 | ||
| # python-impl: CPython | ||
| # - python-version: 3.8 | ||
| # python-release: v3.8 | ||
| # python-impl: CPython | ||
| # - python-version: 3.9 | ||
| # python-release: v3.9 | ||
| # python-impl: CPython | ||
| # - python-version: '3.10' | ||
| # python-release: 'v3.10' | ||
| # python-impl: CPython | ||
| # - python-version: '3.11' | ||
| # python-release: 'v3.11' | ||
| # python-impl: CPython | ||
| - python-version: '3.12' | ||
| python-release: 'v3.12' | ||
| python-impl: CPython | ||
| - python-version: pypy-3.7 | ||
| python-release: v3.7 | ||
| python-impl: PyPy | ||
| - python-version: pypy-3.8 | ||
| python-release: v3.8 | ||
| python-impl: PyPy | ||
| - python-version: pypy-3.9 | ||
| python-release: v3.9 | ||
| python-impl: PyPy | ||
| # - python-version: pypy-3.7 | ||
| # python-release: v3.7 | ||
| # python-impl: PyPy | ||
| # - python-version: pypy-3.8 | ||
| # python-release: v3.8 | ||
| # python-impl: PyPy | ||
| # - python-version: pypy-3.9 | ||
| # python-release: v3.9 | ||
| # python-impl: PyPy | ||
| steps: | ||
| - name: Checkout code | ||
| uses: actions/checkout@v2 | ||
|
|
@@ -174,16 +174,74 @@ jobs: | |
| - name: Install test requirements | ||
| run: python -m pip install -r pyhmmer/tests/requirements.txt | ||
| if: matrix.python-impl == 'CPython' | ||
| - name: Test with coverage | ||
| run: python -m coverage run -m unittest discover -vv | ||
| - name: Upload to Codecov | ||
| uses: codecov/codecov-action@v3 | ||
| if: matrix.python-impl == 'CPython' | ||
| with: | ||
| flags: ${{ matrix.python-release }} | ||
| env_vars: OS | ||
| name: test-python-${{ matrix.python-version }} | ||
| fail_ci_if_error: false | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| codecov_curl_args: "--globoff" | ||
| verbose: true | ||
|
|
||
| # - name: Test Plan7 Background | ||
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_background | ||
|
|
||
| # - name: Test Plan7 Block | ||
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_block | ||
|
|
||
| # - name: Test Plan7 Builder | ||
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_builder | ||
|
|
||
| # - name: Test Plan7 Hit | ||
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_hit | ||
|
|
||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_checksum | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_composition | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_copy | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_eq | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_insert_emissions | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_command_line | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_name | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_accession | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_description | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_consensus | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_set_consensus | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_set_consensus_error | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_write | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_write_empty | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_write_error | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_renormalize | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_scale | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_zero | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_pickle | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_no_cutoffs | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_cutoffs | ||
| - run: python -vd -m unittest -vv pyhmmer.tests.test_plan7.test_hmm.TestHMM.test_cutoffs_pickle | ||
|
|
||
| # - name: Test Plan7 HMMFile | ||
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_hmmfile | ||
|
|
||
| # - name: Test Plan7 OptimizedProfile | ||
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_optimizedprofile | ||
|
|
||
| # - name: Test Plan7 Pipeline | ||
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_pipeline | ||
|
|
||
| # - name: Test Plan7 Profile | ||
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_profile | ||
|
|
||
| # - name: Test Plan7 TopHits | ||
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_tophits | ||
|
|
||
| # - name: Test Plan7 TraceAligner | ||
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_tracealigner | ||
|
|
||
| # - name: Test Plan7 Traces | ||
| # run: python -m unittest -vv pyhmmer.tests.test_plan7.test_traces | ||
|
|
||
| # - name: Test HMMER | ||
| # run: python -m unittest -vv pyhmmer.tests.test_hmmer | ||
| # run: python -m coverage run -m unittest discover -vv | ||
| # - name: Upload to Codecov | ||
| # uses: codecov/codecov-action@v3 | ||
| # if: matrix.python-impl == 'CPython' | ||
| # with: | ||
| # flags: ${{ matrix.python-release }} | ||
| # env_vars: OS | ||
| # name: test-python-${{ matrix.python-version }} | ||
| # fail_ci_if_error: false | ||
| # token: ${{ secrets.CODECOV_TOKEN }} | ||
| # codecov_curl_args: "--globoff" | ||
| # verbose: true | ||